C-di-GMP specific phosphodiesterases

back

YukI


YukI is a dimer with each protomer composed of an EAL domain (with TIM barrel fold), a long helical linker, and a PAS-like domain.

The active site is situated at the C-terminal end of the central β-barrel of the EAL domain. The residues of the active site (here shown with labels) are well conserved, including E33 and L35 of the EAL signature motif.

The c-di-GMP substrate is bound flat upon the actve site with the divalent metal (here Ca++) being sandwiched between binding site and c-di-GMP.

BlrP1


BlrP1

BLUF domain

EAL domain

Active site global view

Active site with labels

Active site + ligand + Mn

Active site + ligand + Mn + HOH

3D structure of YukI
2bas – BsYkuI – Bacillus subtilis

2w27 – BsYkuI + C-di-GMP

3D structure of BlrP1
3gfx, 3gfy, 3gfz, 3gg0, 3gg1 – KpBlrP1 + C-di-GMP - Klebsiella pneumoniae

2kb2 - KpBlrP1 BLUF domain - NMR